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Minor changes + clang-format
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@sergiorg-hpc
sergiorg-hpc committed Jan 18, 2022
1 parent 7d733c6 commit 4d794dd
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Showing 2 changed files with 31 additions and 34 deletions.
14 changes: 7 additions & 7 deletions include/bbp/sonata/report_reader.h
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Original file line number Diff line number Diff line change
Expand Up @@ -98,9 +98,9 @@ class SONATA_API SpikeReader
mutable std::map<std::string, Population> populations_;
};

using Range = std::pair<uint64_t, uint64_t>;
using Ranges = std::vector<Range>;
using NodePointers = std::map<NodeID, Range>;
using Range = std::pair<uint64_t, uint64_t>;
using Ranges = std::vector<Range>;
using NodePointers = std::map<NodeID, Range>;

template <typename KeyType>
class SONATA_API ReportReader
Expand Down Expand Up @@ -166,6 +166,10 @@ class SONATA_API ReportReader
Population(const H5::File& file, const std::string& populationName);
std::pair<size_t, size_t> getIndex(const nonstd::optional<double>& tstart,
const nonstd::optional<double>& tstop) const;
std::pair<NodePointers, Range> getNodePointers(
const nonstd::optional<Selection>& node_ids = nonstd::nullopt) const;
typename DataFrame<KeyType>::DataType getElementIds(const NodePointers& node_pointers,
const Range& range) const;

NodePointers nodes_pointers_;
H5::Group pop_group_;
Expand All @@ -175,10 +179,6 @@ class SONATA_API ReportReader
std::string time_units_;
std::string data_units_;
bool nodes_ids_sorted_ = false;
std::pair<NodePointers, Range> node_pointers_from_selection(
const nonstd::optional<Selection>& node_ids = nonstd::nullopt) const;
typename DataFrame<KeyType>::DataType ids_from_node_pointers(
const std::pair<NodePointers, Range>& result) const;

friend ReportReader;
};
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51 changes: 24 additions & 27 deletions src/report_reader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -285,28 +285,27 @@ std::vector<NodeID> ReportReader<T>::Population::getNodeIds() const {
}

template <typename T>
std::pair<NodePointers, Range> ReportReader<T>::Population::node_pointers_from_selection(
std::pair<NodePointers, Range> ReportReader<T>::Population::getNodePointers(
const nonstd::optional<Selection>& selection) const {
NodePointers node_pointers;
Range range = { std::numeric_limits<uint64_t>::max(),
std::numeric_limits<uint64_t>::min() };
Range range = {std::numeric_limits<uint64_t>::max(), std::numeric_limits<uint64_t>::min()};

const auto& update_range = [&range](const Range range_) {
range.first = std::min(range.first, range_.first);
range.second = std::max(range.second, range_.second);
// Helper function to update the min and max values
const auto& update_range = [&range](const Range range_new) {
range.first = std::min(range.first, range_new.first);
range.second = std::max(range.second, range_new.second);
};

// Take all nodes if no selection is provided
if (!selection) {
node_pointers = nodes_pointers_;

for (const auto& node_pointer : node_pointers) {
update_range(node_pointer.second);
}
}
else if (!selection->empty()) {
} else if (!selection->empty()) {
const auto& node_ids = selection->flatten();

for (const auto& node_id : node_ids) {
const auto it = nodes_pointers_.find(node_id);
if (it != nodes_pointers_.end()) {
Expand All @@ -316,39 +315,37 @@ std::pair<NodePointers, Range> ReportReader<T>::Population::node_pointers_from_s
}
}

return { node_pointers, range };
return {node_pointers, range};
}

template <typename T>
typename DataFrame<T>::DataType ReportReader<T>::Population::ids_from_node_pointers(
const std::pair<NodePointers, Range>& result) const {
typename DataFrame<T>::DataType ReportReader<T>::Population::getElementIds(
const NodePointers& node_pointers, const Range& range) const {
typename DataFrame<T>::DataType ids{};

const auto& node_pointers = result.first;
const auto& min = result.second.first;
const auto& max = result.second.second;

if (!node_pointers.empty())
{
if (!node_pointers.empty()) {
const auto& min = range.first;
const auto& max = range.second;

std::vector<ElementID> element_ids;
auto dataset_elem_ids = pop_group_.getGroup("mapping").getDataSet("element_ids");
dataset_elem_ids.select({min}, {max - min}).read(element_ids);

// Reserve at least (max - min) elements and shrink afterwards
ids.reserve(max - min);

for (const auto& node_pointer : node_pointers) {
const auto& node_id = node_pointer.first;
const auto& range = node_pointer.second;

for (auto i = (range.first - min); i < (range.second - min); i++)
{

for (auto i = (range.first - min); i < (range.second - min); i++) {
ids.emplace_back(make_key<T>(node_id, element_ids[i]));
}
}

ids.shrink_to_fit();
}

return ids;
}

Expand Down Expand Up @@ -390,8 +387,8 @@ std::pair<size_t, size_t> ReportReader<T>::Population::getIndex(
template <typename T>
typename DataFrame<T>::DataType ReportReader<T>::Population::getNodeIdElementIdMapping(
const nonstd::optional<Selection>& selection) const {
const auto& result = node_pointers_from_selection(selection);
return ids_from_node_pointers(result);
const auto& result = getNodePointers(selection);
return getElementIds(result.first, result.second);
}

template <typename T>
Expand All @@ -417,12 +414,12 @@ DataFrame<T> ReportReader<T>::Population::get(const nonstd::optional<Selection>&

// min and max offsets of the node_ids requested are calculated
// to reduce the amount of IO that is brought to memory
const auto& result = node_pointers_from_selection(selection);
const auto& result = getNodePointers(selection);
const auto& node_pointers = result.first;
const auto& min = result.second.first;
const auto& max = result.second.second;

data_frame.ids = ids_from_node_pointers(result);
data_frame.ids = getElementIds(result.first, result.second);
if (data_frame.ids.empty()) { // At the end no data available (wrong node_ids?)
return DataFrame<T>{{}, {}, {}};
}
Expand Down

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